[ensembl-dev] ensembl compara : warning messages

[Benoît Ballester]

Hi Matthieu, 

Thanks for the info,

A+, 

Ben



On 12 Dec 2013, at 23:22, Matthieu Muffato wrote:

> Hi Benoît,
> 
> v73 of the Compara API is indeed more verbose about missing core databases. This exhaustive search is triggered when the API cannot not naturally find a species in the Registry (e.g "homo sapiens" instead of "homo_sapiens", etc).
> 
> We had a few cases in previous releases where the Compara API was not reporting missing links, hence the change in e73. I understand there are too many warnings, and this has been improved in e74. The change was unfortunately too big to backport to e73 after the public release, so I'd suggest you simply comment the line 444 out in GenomeDB.pm
> 
> 
> Hope this helps,
> Matthieu
> 
> 
> On 12/12/13 17:04, Benoît Ballester wrote:
>> Hi everyone,
>> 
>> I am using the v73 API against databases (human + compara) installed on a local server.
>> I do not have all core databases on the server, and I use a registry conf file with just human and compara in it.
>> 
>> I get these warning messages (see below)
>> Could you please advice on how to turn them off please ? I am sure I am missing something obvious.
>> 
>> Thanks,
>> 
>> Ben
>> 
>> 
>> Cannot find the core database of 'pelodiscus_sinensis' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /cobelix/benoit/src/v73/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
>> Cannot find the core database of 'xiphophorus_maculatus' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /cobelix/benoit/src/v73/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
>> Cannot find the core database of 'mustela_putorius_furo' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /cobelix/benoit/src/v73/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
>> Cannot find the core database of 'felis_catus' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /cobelix/benoit/src/v73/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
>> Cannot find the core database of 'rattus_norvegicus' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /cobelix/benoit/src/v73/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
>> Cannot find the core database of 'gallus_gallus' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /cobelix/benoit/src/v73/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
>> Cannot find the core database of 'caenorhabditis_elegans' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /cobelix/benoit/src/v73/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
>> Cannot find the core database of 'anas_platyrhynchos' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /cobelix/benoit/src/v73/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
>> Cannot find the core database of 'ficedula_albicollis' in the Registry. Be aware that getting Core objects from Compara is not possible for this species at /cobelix/benoit/src/v73/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm line 444.
>> 
> 
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--
Benoît Ballester, PhD
Inserm U1090, TAGC
Campus de Luminy
13288 Marseille Cedex 9
France
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